Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

4 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq to investigate how human-specific Notch2 paralogs expand cortical neurogenesis through regulation of Delta/Notch interactions.

ABSTRACT: The human cerebral cortex underwent rapid enlargement and complexification during recent evolution. Hominid-specific (HS) genes arising from genomic duplications may be involved, but it remains unclear how much and which HS genes contribute to human brain development. Using tailored RNAseq profiling, we identify a repertoire of >60 HS genes that display robust and dynamic expression during human fetal corticogenesis. Among these, Notch2NL genes stood out as human-specific Notch2 paralogs that promotes cortical progenitor maintenance. Clonal analyses of human cortical progenitors revealed that Notch2NL promotes their expansion by increasing self-renewal, ultimately leading to higher clonal neuronal output. Notch2NL acts by direct activation of the Notch pathway, through cell-autonomous inhibition of Delta/Notch interactions. Our data identify a large repertoire of newly evolved genes linking human brain development and evolution, and indicate how human-specific Notch paralogs may have contributed to the expansion of the human brain.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Vincent Detours

PROVIDER: E-MTAB-6232 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell analysis of emergent haematopoiesis in the human fetal bone marrow (SS2)

Project description:Haematopoeisis emerges in the human fetal bone marrow (BM) at around 12 post conception weeks. This constitutes the second wave of definitive haematopoiesis following on from the first wave in fetal liver from around 6 post conception weeks. The BM emerges as the dominant site of haematopoiesis, responsible for lifelong blood and immune cell production. Yet, little is known about how the composition of the fetal BM, the microenvironment permissive to establishing haematopoiesis and the interplay with other sites of fetal haematopoiesis in fetal health or disease. Herein we utilise single cell RNA sequencing to describe fetal haematopoeisis throughout gestation and better understand the development of the human immune system.

2021-07-15 | E-MTAB-9801 | biostudies-arrayexpress

RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome [RNA-Seq]

Project description:The second trimester fetal transcriptome can be assessed based on cell-free RNA found within the amniotic fluid supernatant. The objective of this study was to compare the suitability of two technologies for profiling the human fetal transcriptome: RNA-Seq and expression microarray. Comparisons were based on total numbers of gene detected, rank-order gene expression, and functional genomic analysis. Fewer gene transcripts were observed using RNA-Seq than microarray (4,158 vs 8,842). Correlation of total expression within each sample ranged from R=0.43 to R=0.57. On average, there was 59% concordance in gene identity among the top 10% of genes ranked by expression. The RNA-Seq data yielded more significant pathways enrichment within the ?Physiological Systems Development and Function? categories of IPA. Alternative splicing of many well-known genes, including those previously studied in fetal development, such as H19 and IGF2 is detected by RNA-Seq. Also included in this paper is discussion of the technical challenges inherent to working with cell-free fetal RNA and possible solutions. Cell-free fetal RNA from the amniotic fluid supernatant of five second trimester fetuses was divided and prepared in tandem for analysis using either the Illumina HiSeq 2000 or Affymetrix HG-U133 Plus 2.0 GeneChip microarray.

2014-05-27 | E-GEOD-49890 | biostudies-arrayexpress

4sU metabolic labeled transcripts in 65 YRI LCLs

Project description:Noncoding variants play a central role in the genetics of complex traits, but we still lack a full description of the main molecular pathways through which they act. Here we used molecular data to quantify the contribution of cis-acting genetic effects at each major stage of gene regulation from chromatin to proteins, within a population sample of Yoruba lymphoblastoid cell lines (LCLs). We performed 4sU metabolic labeled transcripts in 65 YRI LCLs to identify genetic variants that affect transcription rates. As expected, we found an important contribution of genetic variation via chromatin, contributing â¼65% of eQTLs (expression Quantitative Trait Loci). The remaining eQTLs, which are not asso- ciated with chromatin-level variation, are highly enriched in transcribed regions, and hence may affect expression through co- or post-transcriptional processes. International HapMap lymphoblastoid cell lines (LCLs) derived from YRI (Yoruba in Ibadan, Nigeria); We adapted the 4sU labelling method from (PMID 21516085). Briefly, cell cultures were grown to log phase in volumes sufficient to yield about 300 ng of 4sU-labeled RNA. Cells were incubated with 4sU for the required length of time (0, 30, or 60 minutes), then washed, pelleted, and frozen. Total RNA was extracted, and 4sU-labeled RNA was separated from total RNA using a bead-based biotin-streptavidin purification protocol. We sequenced metabolic labeled transcripts in 65 YRI LCLs 30 minutes and 60 minutes after incubation.

2016-03-29 | E-GEOD-75220 | biostudies-arrayexpress

GPBAR1 agonism has a broad impact on blocking macrophage activation

Project description:Human D14+ / CD16+ monocytes were treated with GPBAR1 agonists or controls, and were stimulated with interferon gamma and LPS. At 6 and 24 hours, the cells were profiled by RNAseq 40 total samples, 5 per group with eight groups. Individual donors used for multiple comparisons, so paired analysis is possible. Control samples include unstimulated cells, and stimulated cells treated with vehicle control (DMSO).

2014-06-10 | E-GEOD-57494 | biostudies-arrayexpress

Mutations in RAS pathway induce synthetic lethality of MEK inhibition with mitochondrial oxidative metabolism in acute myeloid leukemia

Project description:Bulk RNAseq of primary AML samples at diagnosis

2021-12-31 | E-MTAB-10048 | biostudies-arrayexpress

Laser-capture microscopy coupled with Smart-seq2 (LCM-seq) for robust and efficient transcriptomic profiling of mouse and human tissues

Project description:Generally, when LCM is used in diverse transcriptomic analyses, several hundred, if not thousands, of cells are needed to obtain high quality of RNA-seq data. As some cellular populations are very small and tissue often in scarcity, we aimed to carefully document the lowest number of cells needed to retrieve sequencable libraries. We started with capturing 120 cells and subsequently scaled down to 50 cells, 30 cells, 10 cells, 5 cells, 2 cells and finally 1 cell. By optimizing multiple steps in the procedure, including direct lysis of cells without performing RNA isolation, we developed LCM-seq that couples LCM with Smart-seq2 for robust and efficient polyA-based RNA sequencing. We applied LCM-seq to mouse and human neuron samples, and demonstrated that LCM-seq can allow us to acquire high quality RNA-seq data from mouse and human tissues to conduct various transcriptomic studies. Developing new sequencing technology LCM-seq to efficiently sequence mouse and human tissues

2016-07-05 | E-GEOD-76514 | biostudies-arrayexpress

RNAseq of isolated mitotic HeLa cells treated with Actinomycin D

Project description:The goal of this experiment was to assess whether transcription happens during mitosis. For this, we isolated mitotic HeLa cells and treated them with a transcription inhibitor, ActD.

2018-08-28 | E-MTAB-6661 | biostudies-arrayexpress

Viral nucleases reveal an mRNA degradation-transcription feedback loop in mammalian cells

Project description:Gamma-herpesviruses encode a cytoplasmic mRNA-targeting endonuclease, termed SOX, that cleaves the majority of mRNAs within a cell. Cleaved fragments are subsequently degraded by the cellular mRNA degradation machinery. Here, we reveal that mammalian cells respond to this widespread cytoplasmic mRNA decay by altering levels of RNA polymerase II (RNAPII) transcription in the nucleus. Measurements of both RNAPII recruitment to promoters and nascent mRNA synthesis revealed that the majority of affected genes are transcriptionally repressed in SOX-expressing cells. The transcriptional feedback does not occur in response to the initial endonuclease-induced cleavage, but instead to degradation of the cleaved fragments by cellular exonucleases. In particular, Xrn1 catalytic activity is required for transcriptional repression. Notably, viral mRNA transcription escapes decay-induced repression, and this escape requires Xrn1. Collectively, these results indicate that mRNA decay rates impact transcription in mammalian cells, and that gamma-herpesviruses have incorporated this feedback mechanism into their own gene expression strategy. NIH 3T3 cells were mock, WT, or ∆HS infected with MHV68 in duplicate and 4sU-labeled RNA isolated. 4sU-labeled RNA was submitted for sequencing and reads aligned to the mouse genome or MHV68 viral genome. Differential cellular gene expression was determined between mock and WT infected, mock and ∆HS infected, as well as differential viral gene expression between WT and ∆HS.

2015-07-23 | E-GEOD-70481 | biostudies-arrayexpress

PolII transcription factor in Human HeLa S3

Project description:We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human transcription factor PolII in HeLa S3 cells. The PolII ChIP was performed according to the same protocol as used for the STAT1 samples except that the cells were not stimulated using gamma-interferon prior to formaldehyde fixation. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of the PolII transcription factor in Human HeLa S3.

2008-09-16 | E-GEOD-12781 | biostudies-arrayexpress

STAT1 transcription factor in Human HeLa S3

Project description:We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human transcription factor STAT1 in HeLa S3 cells. The STAT1 ChIP was performed using HeLa S3 cells that are stimulated using gamma-interferon. We have also generated a seqenced input DNA dataset for gamma-interferon stimulated HeLa S3 cells. Raw data for this study is available for download from the Short Read Archive database at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP000703. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of the STAT1 transcription factor in Human HeLa S3.

2008-09-15 | E-GEOD-12782 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data